Your message dated Sun, 05 Jan 2020 12:35:19 +0000 with message-id <[email protected]> and subject line Bug#942476: fixed in r-cran-dt 0.11+dfsg-1 has caused the Debian Bug report #942476, regarding r-cran-dt: missing css files and bad path for javascript files to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 942476: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=942476 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: r-cran-dt Version: 0.9+dfsg-1 Severity: normal Hi, I'm trying to use r-cran-dt to generate a report. The Debian package has problems (see the script at the end to reproduce the issue): - one css file is missing: $ Rscript -e "rmarkdown::render('small_test.rmd')" [...] /usr/bin/pandoc +RTS -K512m -RTS small_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output small_test.html --email-obfuscation none --self-contained --standalone --section-divs --template /usr/lib/R/site-library/rmarkdown/rmd/h/default.html --highlight-style tango --css style.css --variable 'theme:cerulean' --include-in-header /tmp/RtmpDhs6QV/rmarkdown-str692d16ebe87a.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/latex-div.lua pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/css/jquery.dataTables.extra.css: openBinaryFile: does not exist (No such file or directory) Erreur : pandoc document conversion failed with error 1 Exécution arrêtée Indeed, jquery.dataTables.extra.css is removed from the Debian r-cran-dt package, however, according to apt-file and https://pacakages.debian.org, no Debian package is providing this file. Continuing with $ sudo touch /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/css/jquery.dataTables.extra.css to workaround this problem - one javascript file is not in the expected path: $ Rscript -e "rmarkdown::render('small_test.rmd')" [...] /usr/bin/pandoc +RTS -K512m -RTS small_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output small_test.html --email-obfuscation none --self-contained --standalone --section-divs --template /usr/lib/R/site-library/rmarkdown/rmd/h/default.html --highlight-style tango --css style.css --variable 'theme:cerulean' --include-in-header /tmp/RtmpI2EroN/rmarkdown-str6bbf3216f5ad.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/latex-div.lua pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/js/jquery.dataTables.min.js: openBinaryFile: does not exist (No such file or directory) Erreur : pandoc document conversion failed with error 1 Exécution arrêtée Indeed, the javascript file is in /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/js/jquery.dataTables.min.js and not /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/jquery.dataTables.min.js Continuing with $ sudo ln -s . /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/js to workarround the problem - another javascript file is still not in the expected place: Rscript -e "rmarkdown::render('small_test.rmd')" [...] /usr/bin/pandoc +RTS -K512m -RTS small_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output small_test.html --email-obfuscation none --self-contained --standalone --section-divs --template /usr/lib/R/site-library/rmarkdown/rmd/h/default.html --highlight-style tango --css style.css --variable 'theme:cerulean' --include-in-header /tmp/RtmpS0d9gK/rmarkdown-str6e161233a5ca.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/latex-div.lua pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/jszip.min.js: openBinaryFile: does not exist (No such file or directory) Erreur : pandoc document conversion failed with error 1 Exécution arrêtée dpkg -S tells me that this file is (on Debian system) in libjs-jquery-datatables-extensions: /usr/share/javascript/jquery-datatables-extensions/JSZip/jszip.min.js (with a copy in 3 others packages on my machine) Continuing with $ sudo ln -s /usr/share/javascript/jquery-datatables-extensions/JSZip/jszip.min.js /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/jszip.min.js to workarround the problem - another javascript file is still not in the expected place: Rscript -e "rmarkdown::render('small_test.rmd')" [...] /usr/bin/pandoc +RTS -K512m -RTS small_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output small_test.html --email-obfuscation none --self-contained --standalone --section-divs --template /usr/lib/R/site-library/rmarkdown/rmd/h/default.html --highlight-style tango --css style.css --variable 'theme:cerulean' --include-in-header /tmp/RtmpMKo2nV/rmarkdown-str6e7f218627e7.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/latex-div.lua pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/pdfmake.min.js: openBinaryFile: does not exist (No such file or directory) Erreur : pandoc document conversion failed with error 1 Exécution arrêtée dpkg -S tells me that this file is (on Debian system) in libjs-jquery-datatables-extensions: /usr/share/javascript/jquery-datatables-extensions/pdfmake/build/pdfmake.min.js Continuing with $ sudo ln -s /usr/share/javascript/jquery-datatables-extensions/pdfmake/build/pdfmake.min.js /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/pdfmake.min.js - another javascript file is missing (vfs_fonts.js) and does not seem to be available in Debian $ Rscript -e "rmarkdown::render('small_test.rmd')" [...] /usr/bin/pandoc +RTS -K512m -RTS small_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output small_test.html --email-obfuscation none --self-contained --standalone --section-divs --template /usr/lib/R/site-library/rmarkdown/rmd/h/default.html --highlight-style tango --css style.css --variable 'theme:cerulean' --include-in-header /tmp/RtmpiA4YrW/rmarkdown-str6ed3608bac42.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/latex-div.lua pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/vfs_fonts.js: openBinaryFile: does not exist (No such file or directory) Erreur : pandoc document conversion failed with error 1 Exécution arrêtée Continuing with $ sudo touch /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/vfs_fonts.js Eventually the html document is generated. So, it seems to me that: - some files are removed from the r-cran-dt source packages whereas they are not provided by any other Debian packages (at least jquery.dataTables.extra.css and vfs_fonts.js) - some files are not available in the expected path (through symlinks), at least jquery.dataTables.min.js, jszip.min.js and pdfmake.min.js Note that removing all workarounds: $ sudo rm /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/css/jquery.dataTables.extra.css /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/js /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/jszip.min.js /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/pdfmake.min.js /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/vfs_fonts.js and installing locally the DT package (install.packages('DT') from R) makes the script working. So the bugs come from the packaging. Regards, Vincent PS: in attachment, the Rcmd script file and the data file to reproduce this bug -- System Information: Debian Release: bullseye/sid APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'oldstable-updates'), (500, 'unstable'), (500, 'testing'), (500, 'stable'), (500, 'oldstable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386, armel, mipsel Kernel: Linux 5.2.0-3-amd64 (SMP w/4 CPU cores) Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8), LANGUAGE=fr_FR.utf8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages r-cran-dt depends on: ii libjs-jquery 3.3.1~dfsg-3 ii libjs-jquery-datatables 1.10.20+dfsg-1 ii libjs-jquery-datatables-extensions 0.0+20150910+dfsg-2 ii libjs-jquery-selectize.js 0.12.6+dfsg-1 ii r-base-core [r-api-3.5] 3.6.1-6 ii r-cran-crosstalk 1.0.0+dfsg-4 ii r-cran-htmltools 0.4.0-1 ii r-cran-htmlwidgets 1.5+dfsg-1 ii r-cran-jsonlite 1.6+dfsg-1 ii r-cran-magrittr 1.5-5 ii r-cran-promises 1.1.0-1 Versions of packages r-cran-dt recommends: ii r-cran-knitr 1.25+dfsg-1 ii r-cran-rmarkdown 1.16+dfsg-1 Versions of packages r-cran-dt suggests: ii r-cran-shiny 1.3.2+dfsg-1 -- no debconf information--- title: "Test" author: "Cellule de Bioinformatique" date: "`r format(Sys.time(), '%d %B %Y')`" output: html_document: theme: cerulean highlight: tango --- ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = FALSE) library(dplyr) library(tidyr) library(DT) ``` # Métriques de séquençage ```{r metrics, echo=FALSE} Identitovigilance = read.delim("Identitovigilance.tsv", header=TRUE) Identitovigilance %>% datatable(extensions = 'Buttons', options = list(dom = 'Bfrtip',buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),pageLength=10, scrollX='400px', columnDefs = list(list(className = 'dt-center', targets = "_all"))),rownames = FALSE) ```Echantillon Sexe Couv. autosomes Couv. chrX NAN094 H 44.2339823740566 22.0109940293309 NAQ095 F 45.6972749039199 45.2938556050553 NAQ102 H 46.4503791247102 23.3367492729385 NAQ104 F 42.6604621137042 41.59214873412 NAQ114 H 47.4454524288081 23.2806965771802 NAQ115 H 45.3128157396608 22.5878060713352 NAQ116 H 44.5120151092971 22.1902206625124 NAQ117 H 44.5667556457501 22.3253287035313 NAQ124 H 44.1547140407541 22.0612210097021 NAQ127 H 45.1406368058383 22.5020949697436 NAQ131 H 45.1472097072126 22.4443120795604 NAQ133 F 41.2195065918166 40.9188784430404 NAQ141 F 42.749084378469 43.7119043619277 NAR013 H 43.5951059938956 21.9606501487595 NAR018 H 45.3550866503083 22.3055364037361 NAR019 H 45.4337543537171 22.9515217254307 NAR028 F 38.4230276904003 37.9964613205878 NAR032 F 44.0734609415596 44.4685709835858 NAR041 F 43.9393289823221 42.9609225995391 NAR046 F 44.1486633776115 43.7450775977989 NAR047 H 43.3750988313457 22.4532127447165 NAR048 F 39.6169267993457 40.7340405197216 NAR053 F 43.2499594551444 42.0961465556751 NAR059 H 41.6948703311421 21.9658016456802
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--- Begin Message ---Source: r-cran-dt Source-Version: 0.11+dfsg-1 We believe that the bug you reported is fixed in the latest version of r-cran-dt, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (supplier of updated r-cran-dt package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 05 Jan 2020 13:02:37 +0100 Source: r-cran-dt Architecture: source Version: 0.11+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <[email protected]> Changed-By: Andreas Tille <[email protected]> Closes: 942476 Changes: r-cran-dt (0.11+dfsg-1) unstable; urgency=medium . * New upstream version * Restrict Files-Excluded to those files that are provided by other packages * Fix links to some JS files Closes: #942476 * Set upstream metadata fields: Bug-Submit, Repository. * Exclude source.min.js (which is hopefully not necessary for every day use Checksums-Sha1: 7705e304215e908e95d882500217f95883378f4c 2268 r-cran-dt_0.11+dfsg-1.dsc e727efd8649ffd67686c022130b1e23832c817f5 70456 r-cran-dt_0.11+dfsg.orig.tar.xz 8d30d01ebb953becef027994ac956be9cbe603f0 30384 r-cran-dt_0.11+dfsg-1.debian.tar.xz d219a35ef4584761421b1f8387c986683cc82dfe 10823 r-cran-dt_0.11+dfsg-1_amd64.buildinfo Checksums-Sha256: 0638f122fe99095f3c2dfce069f691c7f4c74122adcb58cf89f485827ed90bac 2268 r-cran-dt_0.11+dfsg-1.dsc ec8b6142e1484d1c03267a16d7b924b10d5bd844f710341f8e18f9a557adbeb2 70456 r-cran-dt_0.11+dfsg.orig.tar.xz 3082e81a2093580a958c5f46191c901bbbed889a548411df03f0a2ed4e0aa061 30384 r-cran-dt_0.11+dfsg-1.debian.tar.xz fe7f47078ab03907a2eacf5a54a8953c9b2d6bf836e22a8843638bc3d6cf9653 10823 r-cran-dt_0.11+dfsg-1_amd64.buildinfo Files: 91aba2782acfca24a75d70d7b03a1f8d 2268 gnu-r optional r-cran-dt_0.11+dfsg-1.dsc 6a070c4d521c2897425299c7ebe0ea8f 70456 gnu-r optional r-cran-dt_0.11+dfsg.orig.tar.xz ad89551243fcd3b54e59332c69d9961e 30384 gnu-r optional r-cran-dt_0.11+dfsg-1.debian.tar.xz a6ab65f3affce85053e86c184cc69a09 10823 gnu-r optional r-cran-dt_0.11+dfsg-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl4R0mERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFGQA/+Ojwyih4ulLG2JML7USJSqwiS8v9XvaS+ GxoSnABhr8Z4VAsJO3o1WVEI4gCJ75627L6DVWI+FX8RY1Qi7yry0DTJ8Jyo4a7T I/cQmnHE5W6zPc2PXOUArR0sSb0S0/nKOCOKPPBhKJX4WNK0InS8PwID9YXzrsI7 Y0DzNePl8W20+iJ9wS+690fJKieZXxe7Kn7aW2AdOgbX+oyM/JFXi2vvresYfjTX vcJfDHnLJdJMONYRdLhJRGFW4zjtexcc+sYzVko/j0i9su3AHxvc/5j3MaLt2ABd zpWrVjRWFLG0hkz75RdarLSPjyotnmgsmLdQrWPstyfLONOKjVXQ/gTLnHAR7Nmg 686Nx5FusIBX69GrDYua3HOd4Xcg00KsWoON5QCSwLHHfrvNq+F6Qz9WaFKJXny0 ac1oCDspj3HUu59U/oWcyNi9RqBQI1JsVE1oKeYDURiJupNkFswBIxqu0AkGZoJM ulvCcwseyWJXId7xdDrS5/Ti+4T/xbfjqp2EHMQitV2G9cOyXJODLhci3FPNEEns 3qMOT4z16vqCfVDx+o/6G3cxsyK+RTTHj6ub71h29YQ0+b27lQ7sQ7AgJO2CD8FL lx8iagjJuMiatip/lGUlP0ImVh8XhSfFjTof5WXQcu/D116bEju/QRQ2qZZxzG01 rTBXs9OFY/Q= =NigZ -----END PGP SIGNATURE-----
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